We analyze the effects of average index variation on the transmission characteristics of an index-apodized long-period fiber grating (LPFG) by the transfer matrix method and study how these effects depend on the grating length, the grating profile, the modal dispersion factor, and the duty cycle of the index modulation. Apart from shifting the resonance wavelength and modifying the rejection band, average index variation can give rise to significant side lobes that may appear on the short-wavelength or long-wavelength side of the rejection band, depending on the signs of the average index change and the modal dispersion factor. Our results provide general guidance for the writing of LPFGs for the minimization of side lobes. Our analysis compares well with published experimental results and should be useful for the design and fabrication of LPFGs.